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- EMDB-20935: SWI/SNF nucleosome complex with ATP-gamma-S -

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Basic information

Entry
Database: EMDB / ID: EMD-20935
TitleSWI/SNF nucleosome complex with ATP-gamma-S
Map dataSWI/SNF nucleosome complex assembled in the presence of ATP
Sample
  • Complex: SWI/SNF nucleosome complex with ATP-gamma-S
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsHe Y / Han Y
Funding support United States, 3 items
OrganizationGrant numberCountry
American Cancer SocietyIRG-15-173-21 United States
National Institutes of Health/National Cancer InstituteU54CA193419 United States
National Institutes of Health/National Cancer InstituteP01 CA092584 United States
CitationJournal: Nature / Year: 2020
Title: Cryo-EM structure of SWI/SNF complex bound to a nucleosome.
Authors: Yan Han / Alexis A Reyes / Sara Malik / Yuan He /
Abstract: The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel ...The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation.
History
DepositionNov 8, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseMar 25, 2020-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20935.png

Downloads & links

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Map

FileDownload / File: emd_20935.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSWI/SNF nucleosome complex assembled in the presence of ATP
Voxel sizeX=Y=Z: 2.24 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.022585146 - 0.1564821
Average (Standard dev.)0.0014457639 (±0.008131551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 430.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162182277
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0230.1560.001

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Supplemental data

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Sample components

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Entire : SWI/SNF nucleosome complex with ATP-gamma-S

EntireName: SWI/SNF nucleosome complex with ATP-gamma-S
Components
  • Complex: SWI/SNF nucleosome complex with ATP-gamma-S

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Supramolecule #1: SWI/SNF nucleosome complex with ATP-gamma-S

SupramoleculeName: SWI/SNF nucleosome complex with ATP-gamma-S / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
Details: 10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 76.5 e/Å2

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 0.5)
Details: CTF amplitude correction was performed following 3D auto refinement in relion.
Startup modelType of model: OTHER / Details: Ab initio from Cryosparc
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 44035
FSC plot (resolution estimation)

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